Recursiveness, Switching, and Fluctuations in a Replicating Catalytic Network

A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers of molecules and species, three phases are found: fast switching state without recursive production, recursive production, and itinerancy between the above two states. The number distributions of the molecules in the recursive states are shown to be log-normal except for those species that form a core hypercycle, and are explained with the help of a heuristic argument.Comment: 4 pages (with 7 figures (6 color)), submitted to PR

Skeleton and fractal scaling in complex networks

We find that the fractal scaling in a class of scale-free networks originates from the underlying tree structure called skeleton, a special type of spanning tree based on the edge betweenness centrality. The fractal skeleton has the property of the critical branching tree. The original fractal networks are viewed as a fractal skeleton dressed with local shortcuts. An in-silico model with both the fractal scaling and the scale-invariance properties is also constructed. The framework of fractal networks is useful in understanding the utility and the redundancy in networked systems.Comment: 4 pages, 2 figures, final version published in PR

The role of tank-treading motions in the transverse migration of a spheroidal vesicle in a shear flow

The behavior of a spheroidal vesicle, in a plane shear flow bounded from one side by a wall, is analysed when the distance from the wall is much larger than the spheroid radius. It is found that tank treading motions produce a transverse drift away from the wall, proportional to the spheroid eccentricity and the inverse square of the distance from the wall. This drift is independent of inertia, and is completely determined by the characteristics of the vesicle membrane. The relative strength of the contribution to drift from tank-treading motions and from the presence of inertial corrections, is discussed.Comment: 16 pages, 1 figure, Latex. To appear on J. Phys. A (Math. Gen.

Transition to turbulence in particulate pipe flow

We investigate experimentally the influence of suspended particles on the transition to turbulence. The particles are monodisperse and neutrally-buoyant with the liquid. The role of the particles on the transition depends both upon the pipe to particle diameter ratios and the concentration. For large pipe-to-particle diameter ratios the transition is delayed while it is lowered for small ratios. A scaling is proposed to collapse the departure from the critical Reynolds number for pure fluid as a function of concentration into a single master curve.Comment: 4 pages, 4 figure

The effect of atomic electrons on nuclear fission

We calculate correction to the nuclear fission barrier produced by the atomic electrons. The result presented in analytical form is convenient to use in future nuclear calculations. The atomic electrons have a small stabilizing effect on nuclei, increasing lifetime in nuclear fission channel. This effect gives a new instrument to study the fission process.Comment: 4 pages, 1 figur

The Algorithmic Origins of Life

Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and in particular, that top-down (or downward) causation -- where higher-levels influence and constrain the dynamics of lower-levels in organizational hierarchies -- may be a major contributor to the hierarchal structure of living systems. Here we propose that the origin of life may correspond to a physical transition associated with a shift in causal structure, where information gains direct, and context-dependent causal efficacy over the matter it is instantiated in. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some potential novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.Comment: 13 pages, 1 tabl

Banking union in historical perspective: the initiative of the European Commission in the 1960s-1970s

This article shows that planning for the organization of EU banking regulation and supervision did not just appear on the agenda in recent years with discussions over the creation of the eurozone banking union. It unveils a hitherto neglected initiative of the European Commission in the 1960s and early 1970s. Drawing on extensive archival work, this article explains that this initiative, however, rested on a number of different assumptions, and emerged in a much different context. It first explains that the Commission's initial project was not crisis-driven; that it articulated the link between monetary integration and banking regulation; and finally that it did not set out to move the supervisory framework to the supranational level, unlike present-day developments

Neutron Halo Isomers in Stable Nuclei and their Possible Application for the Production of Low Energy, Pulsed, Polarized Neutron Beams of High Intensity and High Brilliance

We propose to search for neutron halo isomers populated via $\gamma$-capture in stable nuclei with mass numbers of about A=140-180 or A=40-60, where the $4s_{1/2}$ or $3s_{1/2}$ neutron shell model state reaches zero binding energy. These halo nuclei can be produced for the first time with new $\gamma$-beams of high intensity and small band width ($\le$ 0.1%) achievable via Compton back-scattering off brilliant electron beams thus offering a promising perspective to selectively populate these isomers with small separation energies of 1 eV to a few keV. Similar to single-neutron halo states for very light, extremely neutron-rich, radioactive nuclei \cite{hansen95,tanihata96,aumann00}, the low neutron separation energy and short-range nuclear force allows the neutron to tunnel far out into free space much beyond the nuclear core radius. This results in prolonged half lives of the isomers for the $\gamma$-decay back to the ground state in the 100 ps-$\mu$s range. Similar to the treatment of photodisintegration of the deuteron, the neutron release from the neutron halo isomer via a second, low-energy, intense photon beam has a known much larger cross section with a typical energy threshold behavior. In the second step, the neutrons can be released as a low-energy, pulsed, polarized neutron beam of high intensity and high brilliance, possibly being much superior to presently existing beams from reactors or spallation neutron sources.Comment: accepted for publication in Applied Physics

Partial inhibition and bilevel optimization in flux balance analysis

Motivation: Within Flux Balance Analysis, the investigation of complex subtasks, such as finding the optimal perturbation of the network or finding an optimal combination of drugs, often requires to set up a bilevel optimization problem. In order to keep the linearity and convexity of these nested optimization problems, an ON/OFF description of the effect of the perturbation (i.e. Boolean variable) is normally used. This restriction may not be realistic when one wants, for instance, to describe the partial inhibition of a reaction induced by a drug.Results: In this paper we present a formulation of the bilevel optimization which overcomes the oversimplified ON/OFF modeling while preserving the linear nature of the problem. A case study is considered: the search of the best multi-drug treatment which modulates an objective reaction and has the minimal perturbation on the whole network. The drug inhibition is described and modulated through a convex combination of a fixed number of Boolean variables. The results obtained from the application of the algorithm to the core metabolism of E.coli highlight the possibility of finding a broader spectrum of drug combinations compared to a simple ON/OFF modeling.Conclusions: The method we have presented is capable of treating partial inhibition inside a bilevel optimization, without loosing the linearity property, and with reasonable computational performances also on large metabolic networks. The more fine-graded representation of the perturbation allows to enlarge the repertoire of synergistic combination of drugs for tasks such as selective perturbation of cellular metabolism. This may encourage the use of the approach also for other cases in which a more realistic modeling is required. \ua9 2013 Facchetti and Altafini; licensee BioMed Central Ltd

The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure